NBIS ID: 1234
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.Rmd documents can be rendered as such:Use <div>content</div> for block content and <span>content</span> for inline content.
For paragraphs, use <p>content</p>. And use classes text-left, text-center and text-right to align text left, center and right respectively.
<p class="text-right" style="background-color: aliceblue">This content is aligned right.</p>
<p class="text-center" style="background-color: aliceblue">This content is aligned center.</p>
This content is aligned right.
This content is aligned center.
Content can be organised into columns using pull-left-XX or pull-right-XX. Classes for 30, 40, 50, 60 and 70 have been implemented for left and right. Note that the total width must sum to 100.
<div class="pull-left-50" style="background-color: aliceblue">This content is pulled left.</div>
<div class="pull-right-50 text-center" style="background-color: aliceblue">This content is pulled right and text centered.</div>
<div class="pull-left-30" style="background-color: aliceblue">This content is pulled left.</div>
<div class="pull-right-70" style="background-color: aliceblue">This content is pulled right.</div>
This is an example of nested columns.
<div class="pull-left-30" style="background-color: aliceblue">This column is pulled left.</div>
<div class="pull-right-70" style="background-color: aliceblue">
This column is pulled right.
<div class="pull-left-50" style="background-color: #d0ece7">
Nested left.
</div>
<div class="pull-right-50" style="background-color: #f2d7d5">
Nested right.
</div>
</div>
Nested left.
Nested right.
Headings can be defined as shown below.
## Level 2 heading
### Level 3 heading
#### Level 4 heading
##### Level 5 heading
###### Level 6 heading
Six custom classes are defined for text scaling. This can be defined inside a paragraph (<p>) or <span>.
<span class="largest">Largest text.</span>
<span class="larger">Larger text.</span>
<span class="large">Large text.</span>
Normal text.
<span class="small">Small text.</span>
<span class="smaller">Smaller text.</span>
<span class="smallest">Smallest text.</span>
Largest text.
Larger text.
Large text.
Normal text.
Small text.
Smaller text.
Smallest text.
A horizontal line can be created using three or more * or -.
***
This is __Bold text__ This is Bold text
This is _Italic text_ This is Italic text
~~Strikethrough~~ text Strikethrough text
This is Subscript H~2~O displayed as H2O
This is Superscript 2^10^ displayed as 210
This is a [link](r-project.org) This is a link
An example of footnote reference 1
> This is a block quote. This
> paragraph has two lines.
>
> 1. This is a list inside a block quote.
> 2. Second item.
This is a block quote. This paragraph has two lines.
- This is a list inside a block quote.
- Second item.
Code can be defined inline where `this` looks like this. R code can be executed inline `r Sys.Date()` producing 2019-11-16. Code can also be defined inside code blocks.
``` This is code ```
This is code
R code is executed inside code blocks like this
```{r}
Sys.Date()
```
which shows the code and output.
## [1] "2019-11-16"
The code and results can be hidden by ```{r,echo=FALSE,results='hide'}`.
Here is another example of executed R code with input and output.
Unordered lists are created using asterisks.
Ordered lists are created using numbers.
Using regular markdown.

The dimensions are based on image and/or fill up the entire available space. You can control the dimension as shown below.
{width=30%}
This image above is now 30% of it’s original width.
This image below is 30% size.
<img src="assets/cover.jpg" style="width:30%;"/>
This image below is 30% size, has shadow and corners rounded.
<img src="assets/cover.jpg" style="width:30%;" class="fancyimage"/>
R chunks in RMarkdown can be used to control image display size using the arguemnt out.width.
This image below is displayed at a size of 300 pixels.
```{r,out.width=300}
knitr::include_graphics('assets/cover.jpg')
```
This image below is displayed at a size of 75 pixels.
```{r,out.width=75}
knitr::include_graphics('assets/cover.jpg')
```
Some examples of rendering equations.
$e^{i\pi} + 1 = 0$
\(e^{i\pi} + 1 = 0\)
$$\frac{E \times X^2 \prod I}{2+7} = 432$$
\[\frac{E \times X^2 \prod I}{2+7} = 432\]
$$\sum_{i=1}^n X_i$$
\[\sum_{i=1}^n X_i\]
$$\int_0^{2\pi} \sin x~dx$$
\[\int_0^{2\pi} \sin x~dx\]
$\left( \sum_{i=1}^{n}{i} \right)^2 = \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4}$
\(\left( \sum_{i=1}^{n}{i} \right)^2 = \left( \frac{n(n-1)}{2}\right)^2 = \frac{n^2(n-1)^2}{4}\)
$\begin{eqnarray} X & \sim & \mathrm{N}(0,1)\\ Y & \sim & \chi^2_{n-p}\\ R & \equiv & X/Y \sim t_{n-p} \end{eqnarray}$
\(\begin{eqnarray} X & \sim & \mathrm{N}(0,1)\\ Y & \sim & \chi^2_{n-p}\\ R & \equiv & X/Y \sim t_{n-p} \end{eqnarray}\)
$\begin{eqnarray} P(|X-\mu| > k) & = & P(|X-\mu|^2 > k^2)\\ & \leq & \frac{\mathbb{E}\left[|X-\mu|^2\right]}{k^2}\\ & \leq & \frac{\mathrm{Var}[X]}{k^2} \end{eqnarray}$
\(\begin{eqnarray} P(|X-\mu| > k) & = & P(|X-\mu|^2 > k^2)\\ & \leq & \frac{\mathbb{E}\left[|X-\mu|^2\right]}{k^2}\\ & \leq & \frac{\mathrm{Var}[X]}{k^2} \end{eqnarray}\)
View of the data using paged tables. This is the default output for RMarkdown.
Tab. 1: Table using paged tibble.
The most simple table using kable from R package knitr.
| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species |
|---|---|---|---|---|
| 5.1 | 3.5 | 1.4 | 0.2 | setosa |
| 4.9 | 3.0 | 1.4 | 0.2 | setosa |
| 4.7 | 3.2 | 1.3 | 0.2 | setosa |
| 4.6 | 3.1 | 1.5 | 0.2 | setosa |
| 5.0 | 3.6 | 1.4 | 0.2 | setosa |
| 5.4 | 3.9 | 1.7 | 0.4 | setosa |
More advanced table using kableExtra and formattable.
Tab. 2: Table using kableextra.
| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species |
|---|---|---|---|---|
| 5.1 | 3.5 | 1.4 | 0.2 | setosa |
| 4.9 | 3.0 | 1.4 | 0.2 | setosa |
| 4.7 | 3.2 | 1.3 | 0.2 | setosa |
| 4.6 | 3.1 | 1.5 | 0.2 | setosa |
| 7.0 | 3.2 | 4.7 | 1.4 | versicolor |
| 6.4 | 3.2 | 4.5 | 1.5 | versicolor |
| 6.9 | 3.1 | 4.9 | 1.5 | versicolor |
| 6.5 | 3.0 | 5.8 | 2.2 | virginica |
| 7.6 | 3.0 | 6.6 | 2.1 | virginica |
| 4.9 | 2.5 | 4.5 | 1.7 | virginica |
| 7.3 | 2.9 | 6.3 | 1.8 | virginica |
Fig. 1: Static plot using base plot.
R package ggplot2 is one of the most versatile and complete plotting solutions.
Fig. 2: Static plot using ggplot2.
R package highcharter is a wrapper around javascript library highcharts.
Fig. 3: Interactive scatterplot using highcharter.
R package plotly provides R binding around javascript plotting library plotly.
Fig. 4: Interactive scatterplot using plotly.
plotly also has a function called ggplotly which converts a static ggplot2 object into an interactive plot.
Fig. 5: Interactive scatterplot using ggplotly.
ggiraph is also an R package that can be used to convert a static ggplot2 object into an interactive plot.
Fig. 6: Interactive scatterplot using ggiraph.
R package dygraphs provides R bindings for javascript library dygraphs for time series data.
Fig. 7: Interactive time series plot using dygraph.
R package networkD3 allows the use of interactive network graphs from the D3.js javascript library.
Fig. 8: Interactive network plot.
R package leaflet provides R bindings for javascript mapping library; leafletjs.
R package crosstalk allows crosstalk enabled plotting libraries to be linked. Through the shared ‘key’ variable, data points can be manipulated simultaneously on two independent plots.
Fig. 10: Linking independent plots using crosstalk.
css: ["default", "my-theme.css"]pagedown::chrome_print("report.html",output="report.pdf")echo=FALSE in code chunks to hide input code.df_print: default.Built on: 16-Nov-2019.
2019 • SciLifeLab • NBIS
That reference refers to this footnote.↩